The calcareous sponges are represented by about 500 exclusively marine species, distributed in all oceans. Class Calcarea Bowerbank, 1864 includes two subclasses: Calcinea Bidder, 1898 and Calcaronea Bidder, 1898. The Calcarea has a reputation of being obscure and taxonomically difficult because these animals offer very few morphological characters for reliable phylogenetic reconstruction. Many different species were lumped into synonymy, as their diagnostic morphological differences were reinterpreted as a result of intraspecific variability. Recent morphological and molecular analyses have demonstrated that enormous morphological variability of sponges is not the rule and that highly variable and widely distributed sponge species were not as common as previously thought. Together with detailed histology, molecular data appear to be essential to provide substantial evidence for phylogenetic hypoteses based only on molecular methods. Genus Clathrina has one of the most difficult systematic arrangements in the Porifera, within the class Calcarea. It is defined almost exclusively by negative characters and has the simplest organization among sponges – the asconoid aquiferous system – which means that all the cavities are lined by choanocytes. Its skeleton is also very simple, comprising only a few spicule types: diactine, triactine and/or tetractine. The absence of many morphological characters produces the difficult systematics of the genus. In this study we investigated the taxonomic status of 4 distinct morphotypes from the genus Clathrina along the northeastern Adriatic coast, through the observation of external morphologic characters, skeletal architecture and comparison of sequences of the rDNA ITS1-5.8S-ITS2, 18S and 28S.